AFNI program: 3dSynthesize

Output of -help

Usage: 3dSynthesize options
Reads a '-cbucket' dataset and a '.xmat.1D' matrix from 3dDeconvolve,
and synthesizes a fit dataset using selected sub-bricks and
matrix columns.

Options (actually, the first 3 are mandatory)
---------------------------------------------
-cbucket ccc = Read the dataset 'ccc', which should have been
output from 3dDeconvolve via the '-cbucket' option.
-matrix mmm = Read the matrix 'mmm', which should have been
output from 3dDeconvolve via the '-x1D' option.
-select sss = Selects specific columns from the matrix (and the
corresponding coefficient sub-bricks from the
cbucket). The string 'sss' can be of the forms:
baseline = All baseline coefficients.
polort = All polynomial baseline coefficients
(skipping -stim_base coefficients).
allfunc = All coefficients that are NOT marked
(in the -matrix file) as being in
the baseline (i.e., all -stim_xxx
values except those with -stim_base)
allstim = All -stim_xxx coefficients, including
those with -stim_base.
all = All coefficients (should give results
equivalent to '3dDeconvolve -fitts').
something = All columns/coefficients that match
this -stim_label from 3dDeconvolve
[to be precise, all columns whose ]
[-stim_label starts with 'something']
[will be selected for inclusion. ]
digits = Columns can also be selected by
numbers (starting at 0), or number
ranges of the form 3..7 and 3-7.
[A string is a number range if it]
[comprises only digits and the ]
[characters '.' and/or '-'. ]
[Otherwise, it is used to match ]
[a -stim_label. ]
More than one '-select sss' option can be used, or
you can put more than one string after the '-select',
as in this example:
3dSynthesize -matrix fred.xmat.1D -cbucket fred+orig \
-select baseline FaceStim -prefix FS
which synthesizes the baseline and 'FaceStim'
responses together, ignoring any other stimuli
in the dataset and matrix.
-dry = Don't compute the output, just check the inputs.
-TR dt = Set TR in the output to 'dt'. The default value
of TR is read from the header of the matrix file.
-prefix ppp = Output result into dataset with name 'ppp'.

-cenfill xxx = Determines how censored time points from the3dDeconvolve run will be filled. 'xxx' is one of:
zero = 0s will be put in at all censored times
nbhr = average of non-censored neighboring times
none = don't put the censored times in at all
(in which case the created dataset is)
(shorter than the input to 3dDeconvolve)
If you don't give some -cenfill option, the default
operation is 'zero'. This default is different than
previous versions of this program, which did 'none'.
**N.B.: You might like the program to compute the model fit
at the censored times, like it does at all others.
This CAN be done if you input the matrix file saved
by the '-x1D_uncensored' option in 3dDeconvolve.

NOTES:
-- You could do the same thing in 3dcalc, but this way is simpler
and faster. But less flexible, of course.
-- The output dataset is always stored as floats.
-- The -cbucket dataset must have the same number of sub-bricks as
the input matrix has columns.
-- Each column in the matrix file is a time series, used to model
some component of the data time series at each voxel.
-- The sub-bricks of the -cbucket dataset give the weighting
coefficients for these model time series, at each voxel.
-- If you want to calculate a time series dataset wherein the original
time series data has the baseline subtracted, then you could
use 3dSynthesize to compute the baseline time series dataset, and
then use 3dcalc to subtract that dataset from the original dataset.
-- Other similar applications are left to your imagination.
-- To see the column labels stored in matrix file 'fred.xmat.1D', type
the Unix command 'grep ColumnLabels fred.xmat.1D'; sample output:
# ColumnLabels = "Run#1Pol#0 ; Run#1Pol#1 ; Run#2Pol#0 ; Run#2Pol#1 ;
FaceStim#0 ; FaceStim#1 ; HouseStim#0 ; HouseStim#1"
which shows the 4 '-polort 1' baseline parameters from 2 separate
imaging runs, and then 2 parameters each for 'FaceStim' and
'HouseStim'.
-- The matrix file written by 3dDeconvolve has an XML-ish header
before the columns of numbers, stored in '#' comment lines.
If you want to generate your own 'raw' matrix file, without this
header, you can still use 3dSynthesize, but then you can only use
numeric '-select' options (or 'all').
-- When using a 'raw' matrix, you'll probably also want the '-TR' option.
-- When putting more than one string after '-select', do NOT combine
these separate strings togther in quotes. If you do, they will be
seen as a single string, which almost surely won't match anything.
-- Author: RWCox -- March 2007